Abstract 3400: Recurrent focal copy-number changes and loss-of-heterozygosity implicate two non-coding RNAs and one tumor-suppressor gene at chromosome 3q13.31 in osteosarcoma
Bibliographic record
Abstract
Abstract Osteosarcomas are copy-number alteration (CNA)-rich malignant bone tumors. Using microarrays, fluorescence in-situ hybridization and quantitative polymerase chain reaction we characterize a focal region of chr3q13.31 (osteo3q13.31) harboring CNAs in 80% of osteosarcomas. As such, osteo3q13.31 is the most altered region in osteosarcoma and contests the view that CNAs in osteosarcoma are non-recurrent. Most (67%) osteo3q13.31 CNAs are deletions, 75% of which are mono-allelic, and are frequently accompanied by loss-of-heterozygosity (LOH) in flanking DNA. These CNAs often involve the non-coding RNAs (ncRNAs) LOC285194 and BC040587, and sometimes, the limbic system-associated membrane protein (LSAMP) tumor suppressor (TS). Change in expression of osteo3q13.31 genes is ubiquitous in osteosarcoma, usually involving loss of expression. Underscoring the functional significance of osteo3q13.31 CNAs, expression of LOC285194 and BC040587 and sometimes LSAMP, correlates with the presence of osteo3q13.31 CNAs. Focal osteo3q13.31 CNAs and LOH are also common in cell lines from other cancers, identifying osteo3q13.31 as a universal candidate TS region. Osteo3q13.31 genes may function as a unit, since we demonstrate significant correlation between the expression of distantly spaced LSAMP, LOC285194, and BC040587. Supporting this notion, depletion of either LSAMP or LOC285194 promotes proliferation of normal osteoblasts through regulation of apoptotic and cell cycle transcripts, and vascular endothelial growth factor (VEGF)/VEGF receptor 1 (VEGFR1). Furthermore, the presence of LOC285194 or BC040587 deletions in tumor DNA is associated with poor survival of osteosarcoma patients. Osteo3q13.31 therefore represents a novel universal TS region containing several cooperatively acting genes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3400.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".